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Revision 7555

Added inputs/HVAA/

View differences:

inputs/HVAA/Source/map.csv
1
HVAA,VegCore,Filter,Comments
2
:herbarium,referenceType,,
3
:specimen,observationGranularity,,
inputs/HVAA/Source/VegBIEN.csv
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HVAA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
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:specimen,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/observationtype",
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:herbarium,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype",
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:specimen,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/cond/_eq:[right=plot]/left",
inputs/HVAA/Source/test.xml.ref
1
Put template:
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<VegBIEN>
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    <_setDefault id="-1">
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        <source_id><source><shortname>HVAA</shortname></source></source_id>
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        <path>
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            <_simplifyPath>
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                <next>parent_id</next>
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                <path>
9
                    <source>
10
                        <shortname>HVAA</shortname>
11
                        <observationtype>specimen</observationtype>
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                        <sourcetype>herbarium</sourcetype>
13
                    </source>
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                </path>
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            </_simplifyPath>
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        </path>
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    </_setDefault>
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</VegBIEN>
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Inserted 0 new rows into database
inputs/HVAA/Specimen/map.csv
1
HVAA,VegCore,Filter,Comments
2
institutionCode,custodialInstitutions,,
3
collectionCode,collection,,
4
basisOfRecord,basisOfRecord,,
5
catalogNumber,catalogNumber,,
6
otherCatalogNumbers,otherCatalogNumbers,,
7
ownerInstitutionCode,ownerInstitutionCode,,
8
family,family,,
9
scientificName,scientificName,,
10
genus,genus,,
11
specificEpithet,specificEpithet,,
12
taxonRank,taxonRank,,
13
infraspecificEpithet,infraspecificEpithet,,
14
scientificNameAuthorship,scientificNameAuthorship,,
15
taxonRemarks,taxonRemarks,,
16
identifiedBy,identifiedBy,,
17
dateIdentified,dateIdentified,,
18
identificationReferences,identificationReferences,,
19
identificationRemarks,identificationRemarks,,
20
identificationQualifier,identificationQualifier,,
21
typeStatus,typeStatus,,
22
recordedBy,recordedBy,,
23
recordNumber,collectorNumber,,
24
eventDate,eventDate,,
25
year,year,,
26
month,month,,
27
day,day,,
28
startDayOfYear,startDayOfYear,,
29
endDayOfYear,endDayOfYear,,
30
verbatimEventDate,verbatimEventDate,,
31
habitat,habitat,,
32
fieldNotes,organismNotes,,
33
fieldNumber,collectorNumber,,
34
occurrenceRemarks,occurrenceRemarks,,
35
dynamicProperties,dynamicProperties,,
36
associatedTaxa,associatedTaxa,,
37
reproductiveCondition,reproductiveCondition,,
38
establishmentMeans,establishmentMeans,,
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lifeStage,lifeStage,,
40
sex,sex,,
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individualCount,individualCount,,
42
samplingProtocol,samplingProtocol,,
43
preparations,preparations,,
44
country,country,,
45
stateProvince,stateProvince,,
46
county,county,,
47
municipality,municipality,,
48
locality,locality,,
49
decimalLatitude,decimalLatitude,,
50
decimalLongitude,decimalLongitude,,
51
geodeticDatum,geodeticDatum,,
52
coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,,
53
footprintWKT,footprintWKT,,
54
coordinatePrecision,*coordinatePrecision,,
55
locationRemarks,locationRemarks,,
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verbatimCoordinates,verbatimCoordinates,,
57
verbatimCoordinateSystem,verbatimCoordinateSystem,,
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georeferencedBy,georeferencedBy,,
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georeferenceProtocol,georeferenceProtocol,,
60
georeferenceSources,georeferenceSources,,
61
georeferenceVerificationStatus,georeferenceVerificationStatus,,
62
georeferenceRemarks,georeferenceRemarks,,
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minimumElevationInMeters,minimumElevationInMeters,,
64
maximumElevationInMeters,maximumElevationInMeters,,
65
verbatimElevation,verbatimElevation,,
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disposition,disposition,,
67
modified,modified,,
68
language,language,,
69
rights,rights,,
70
rightsHolder,rightsHolder,,
71
accessRights,accessRights,,
72
symbiotaId,occurrenceID,,
inputs/HVAA/Specimen/VegBIEN.csv
1
HVAA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
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catalogNumber,"/_if[@name=""if specimen""]/cond/_exists",
3
symbiotaId,"/_if[@name=""if specimen""]/cond/_exists",
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institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",
5
symbiotaId,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1",
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catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",
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catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
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symbiotaId,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
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institutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/2",
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collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1",
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catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else",
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rights,/location/accessconditions,
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accessRights,/location/accesslevel,
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verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value",
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maximumElevationInMeters,/location/elevation_m/_alt/2/_avg/max,
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minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min,
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fieldNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
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recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
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symbiotaId,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
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locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1,
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habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3,
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samplingProtocol,/location/locationevent/*_id/method/name,
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eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists",
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eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value",
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eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value",
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eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value,
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eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value,
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dateIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value",
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taxonRemarks,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/notes",
30
identificationQualifier,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit",
31
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
32
fieldNotes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes,
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fieldNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2,
34
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2,
35
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections"
36
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
37
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
38
fieldNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else",
39
recordNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else",
40
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
41
symbiotaId,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
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institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2",
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institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value",
44
symbiotaId,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
45
fieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
46
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
47
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",
48
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
49
fieldNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
50
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
51
symbiotaId,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
52
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value",
53
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value",
54
symbiotaId,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
55
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
56
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
57
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
58
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
59
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",
60
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
61
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
62
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
63
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
64
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
65
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2,
66
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
67
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
68
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
69
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2,
70
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2,
71
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,
72
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
73
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
74
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
75
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
76
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
77
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
78
taxonRemarks,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/notes,
79
identificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
80
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
81
fieldNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then",
82
recordNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then",
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locality,/location/locationnarrative/_merge/1,
84
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
85
coordinateUncertaintyInMeters,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value,
86
footprintWKT,/location/locationplace/*_id/place/*_id/coordinates/footprintgeometry_dwc,
87
decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value",
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decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value",
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verbatimCoordinates,/location/locationplace/*_id/place/*_id/coordinates/verbatimcoordinates,
90
country,/location/locationplace/*_id/place/country,
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county,/location/locationplace/*_id/place/county,
92
decimalLatitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"
93
decimalLongitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"
94
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2,
95
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2,
96
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2,
97
stateProvince,/location/locationplace/*_id/place/stateprovince,
98
locationRemarks,/location/notespublic,
99
verbatimElevation,/location/verbatimelevation,
100
associatedTaxa,,** No join mapping for associatedTaxa ** 
101
basisOfRecord,,** No join mapping for basisOfRecord ** 
102
coordinatePrecision,,** No join mapping for *coordinatePrecision ** 
103
day,,** No join mapping for day ** 
104
disposition,,** No join mapping for disposition ** 
105
dynamicProperties,,** No join mapping for dynamicProperties ** 
106
endDayOfYear,,** No join mapping for endDayOfYear ** 
107
geodeticDatum,,** No join mapping for geodeticDatum ** 
108
georeferenceProtocol,,** No join mapping for georeferenceProtocol ** 
109
georeferenceRemarks,,** No join mapping for georeferenceRemarks ** 
110
georeferenceSources,,** No join mapping for georeferenceSources ** 
111
georeferenceVerificationStatus,,** No join mapping for georeferenceVerificationStatus ** 
112
georeferencedBy,,** No join mapping for georeferencedBy ** 
113
identificationReferences,,** No join mapping for identificationReferences ** 
114
identificationRemarks,,** No join mapping for identificationRemarks ** 
115
language,,** No join mapping for language ** 
116
lifeStage,,** No join mapping for lifeStage ** 
117
modified,,** No join mapping for modified ** 
118
month,,** No join mapping for month ** 
119
municipality,,** No join mapping for municipality ** 
120
occurrenceRemarks,,** No join mapping for occurrenceRemarks ** 
121
otherCatalogNumbers,,** No join mapping for otherCatalogNumbers ** 
122
ownerInstitutionCode,,** No join mapping for ownerInstitutionCode ** 
123
preparations,,** No join mapping for preparations ** 
124
reproductiveCondition,,** No join mapping for reproductiveCondition ** 
125
rightsHolder,,** No join mapping for rightsHolder ** 
126
startDayOfYear,,** No join mapping for startDayOfYear ** 
127
typeStatus,,** No join mapping for typeStatus ** 
128
verbatimCoordinateSystem,,** No join mapping for verbatimCoordinateSystem ** 
129
verbatimEventDate,,** No join mapping for verbatimEventDate ** 
130
year,,** No join mapping for year ** 
inputs/HVAA/Specimen/test.xml.ref
1
Put template:
2
<VegBIEN>
3
    <_setDefault id="-1">
4
        <source_id><source><shortname>HVAA</shortname></source></source_id>
5
        <path>
6
            <_simplifyPath>
7
                <next>parent_id</next>
8
                <path>
9
                    <location>
10
                        <authorlocationcode>
11
                            <_alt>
12
                                <1>$symbiotaId</1>
13
                                <2>
14
                                    <_join>
15
                                        <1>$institutionCode</1>
16
                                        <2>$collectionCode</2>
17
                                        <3>$catalogNumber</3>
18
                                    </_join>
19
                                </2>
20
                            </_alt>
21
                        </authorlocationcode>
22
                        <accessconditions>$rights</accessconditions>
23
                        <accesslevel>$accessRights</accesslevel>
24
                        <elevation_m>
25
                            <_alt>
26
                                <1>
27
                                    <_units>
28
                                        <to>m</to>
29
                                        <to></to>
30
                                        <value>$verbatimElevation</value>
31
                                    </_units>
32
                                </1>
33
                                <2>
34
                                    <_avg>
35
                                        <max>$maximumElevationInMeters</max>
36
                                        <min>$minimumElevationInMeters</min>
37
                                    </_avg>
38
                                </2>
39
                            </_alt>
40
                        </elevation_m>
41
                        <iscultivated>
42
                            <_locationnarrative_is_cultivated>
43
                                <locationnarrative>
44
                                    <_join>
45
                                        <1>$locality</1>
46
                                        <3>$habitat</3>
47
                                    </_join>
48
                                </locationnarrative>
49
                            </_locationnarrative_is_cultivated>
50
                        </iscultivated>
51
                        <locationevent>
52
                            <method_id><method><name>$samplingProtocol</name></method></method_id>
53
                            <obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate>
54
                            <obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate>
55
                            <taxonoccurrence>
56
                                <aggregateoccurrence>
57
                                    <count>$individualCount</count>
58
                                    <notes>$fieldNotes</notes>
59
                                    <plantobservation>
60
                                        <authorplantcode>
61
                                            <_alt>
62
                                                <0>$fieldNumber</0>
63
                                                <1>$recordNumber</1>
64
                                            </_alt>
65
                                        </authorplantcode>
66
                                        <definedvalue fkey="tablerecord_id">
67
                                            <userdefined_id>
68
                                                <userdefined>
69
                                                    <tablename>plantobservation</tablename>
70
                                                    <userdefinedname>sex</userdefinedname>
71
                                                </userdefined>
72
                                            </userdefined_id>
73
                                            <definedvalue>$sex</definedvalue>
74
                                        </definedvalue>
75
                                        <specimenreplicate>
76
                                            <catalognumber_dwc>$catalogNumber</catalognumber_dwc>
77
                                            <collectioncode_dwc>$collectionCode</collectioncode_dwc>
78
                                            <collectionnumber>
79
                                                <_alt>
80
                                                    <0>$fieldNumber</0>
81
                                                    <1>$recordNumber</1>
82
                                                </_alt>
83
                                            </collectionnumber>
84
                                            <institution_id>
85
                                                <sourcelist>
86
                                                    <name>$institutionCode</name>
87
                                                    <sourcename>
88
                                                        <name>
89
                                                            <_split>
90
                                                                <separator>[,;] *</separator>
91
                                                                <value>$institutionCode</value>
92
                                                            </_split>
93
                                                        </name>
94
                                                    </sourcename>
95
                                                </sourcelist>
96
                                            </institution_id>
97
                                            <sourceaccessioncode>$symbiotaId</sourceaccessioncode>
98
                                        </specimenreplicate>
99
                                    </plantobservation>
100
                                </aggregateoccurrence>
101
                                <collector_id><party><fullname>$recordedBy</fullname></party></collector_id>
102
                                <iscultivated>
103
                                    <_map>
104
                                        <cultivated>t</cultivated>
105
                                        <wild>f</wild>
106
                                        <*></*>
107
                                        <value>$establishmentMeans</value>
108
                                    </_map>
109
                                </iscultivated>
110
                                <isnative>
111
                                    <_map>
112
                                        <native>t</native>
113
                                        <exotic>f</exotic>
114
                                        <*></*>
115
                                        <value>$establishmentMeans</value>
116
                                    </_map>
117
                                </isnative>
118
                                <sourceaccessioncode>$symbiotaId</sourceaccessioncode>
119
                                <taxondetermination>
120
                                    <party_id><party><fullname>$identifiedBy</fullname></party></party_id>
121
                                    <taxonverbatim_id>
122
                                        <taxonverbatim>
123
                                            <taxonlabel_id>
124
                                                <taxonlabel>
125
                                                    <parent_id>
126
                                                        <taxonlabel>
127
                                                            <rank>$taxonRank</rank>
128
                                                            <parent_id>
129
                                                                <taxonlabel>
130
                                                                    <rank>cultivar</rank>
131
                                                                    <parent_id>
132
                                                                        <taxonlabel>
133
                                                                            <rank>forma</rank>
134
                                                                            <parent_id>
135
                                                                                <taxonlabel>
136
                                                                                    <rank>variety</rank>
137
                                                                                    <parent_id>
138
                                                                                        <taxonlabel>
139
                                                                                            <rank>subspecies</rank>
140
                                                                                            <parent_id>
141
                                                                                                <taxonlabel>
142
                                                                                                    <rank>species</rank>
143
                                                                                                    <taxonepithet>$specificEpithet</taxonepithet>
144
                                                                                                    <parent_id>
145
                                                                                                        <taxonlabel>
146
                                                                                                            <rank>genus</rank>
147
                                                                                                            <taxonepithet>$genus</taxonepithet>
148
                                                                                                            <parent_id>
149
                                                                                                                <taxonlabel>
150
                                                                                                                    <rank>family</rank>
151
                                                                                                                    <taxonepithet>$family</taxonepithet>
152
                                                                                                                </taxonlabel>
153
                                                                                                            </parent_id>
154
                                                                                                        </taxonlabel>
155
                                                                                                    </parent_id>
156
                                                                                                </taxonlabel>
157
                                                                                            </parent_id>
158
                                                                                        </taxonlabel>
159
                                                                                    </parent_id>
160
                                                                                </taxonlabel>
161
                                                                            </parent_id>
162
                                                                        </taxonlabel>
163
                                                                    </parent_id>
164
                                                                </taxonlabel>
165
                                                            </parent_id>
166
                                                            <taxonepithet>$infraspecificEpithet</taxonepithet>
167
                                                        </taxonlabel>
168
                                                    </parent_id>
169
                                                    <rank>$taxonRank</rank>
170
                                                    <taxonomicname>
171
                                                        <_merge_prefix>
172
                                                            <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
173
                                                            <value>
174
                                                                <_alt>
175
                                                                    <1>$scientificName</1>
176
                                                                    <2>
177
                                                                        <_join_words>
178
                                                                            <1>
179
                                                                                <_join_words>
180
                                                                                    <2>$genus</2>
181
                                                                                    <3>$specificEpithet</3>
182
                                                                                    <5>
183
                                                                                        <_join_words>
184
                                                                                            <1>
185
                                                                                                <_if name="if has infraspecificEpithet">
186
                                                                                                    <cond>$infraspecificEpithet</cond>
187
                                                                                                    <then>$taxonRank</then>
188
                                                                                                </_if>
189
                                                                                            </1>
190
                                                                                            <2>$infraspecificEpithet</2>
191
                                                                                        </_join_words>
192
                                                                                    </5>
193
                                                                                </_join_words>
194
                                                                            </1>
195
                                                                            <2>$scientificNameAuthorship</2>
196
                                                                        </_join_words>
197
                                                                    </2>
198
                                                                </_alt>
199
                                                            </value>
200
                                                        </_merge_prefix>
201
                                                    </taxonomicname>
202
                                                </taxonlabel>
203
                                            </taxonlabel_id>
204
                                            <author>$scientificNameAuthorship</author>
205
                                            <family>$family</family>
206
                                            <genus>$genus</genus>
207
                                            <specific_epithet>$specificEpithet</specific_epithet>
208
                                            <taxonomicname>$scientificName</taxonomicname>
209
                                            <verbatimrank>$taxonRank</verbatimrank>
210
                                        </taxonverbatim>
211
                                    </taxonverbatim_id>
212
                                    <determinationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></determinationdate>
213
                                    <notes>$taxonRemarks</notes>
214
                                    <taxonfit>$identificationQualifier</taxonfit>
215
                                </taxondetermination>
216
                            </taxonoccurrence>
217
                        </locationevent>
218
                        <locationnarrative>
219
                            <_merge>
220
                                <1>$locality</1>
221
                                <3>
222
                                    <_label>
223
                                        <label>habitat</label>
224
                                        <value>$habitat</value>
225
                                    </_label>
226
                                </3>
227
                            </_merge>
228
                        </locationnarrative>
229
                        <locationplace>
230
                            <place_id>
231
                                <place>
232
                                    <coordinates_id>
233
                                        <coordinates>
234
                                            <coordsaccuracy_m><_noCV><value>$coordinateUncertaintyInMeters</value></_noCV></coordsaccuracy_m>
235
                                            <footprintgeometry_dwc>$footprintWKT</footprintgeometry_dwc>
236
                                            <latitude_deg>
237
                                                <_nullIf>
238
                                                    <null>0</null>
239
                                                    <type>float</type>
240
                                                    <value>$decimalLatitude</value>
241
                                                </_nullIf>
242
                                            </latitude_deg>
243
                                            <longitude_deg>
244
                                                <_nullIf>
245
                                                    <null>0</null>
246
                                                    <type>float</type>
247
                                                    <value>$decimalLongitude</value>
248
                                                </_nullIf>
249
                                            </longitude_deg>
250
                                            <verbatimcoordinates>$verbatimCoordinates</verbatimcoordinates>
251
                                        </coordinates>
252
                                    </coordinates_id>
253
                                    <country>$country</country>
254
                                    <county>$county</county>
255
                                    <matched_place_id>
256
                                        <place>
257
                                            <source_id><source><shortname>geoscrub</shortname></source></source_id>
258
                                            <coordinates_id>
259
                                                <coordinates>
260
                                                    <source_id><source><shortname>geoscrub</shortname></source></source_id>
261
                                                    <latitude_deg>
262
                                                        <_nullIf>
263
                                                            <null>0</null>
264
                                                            <type>float</type>
265
                                                            <value>$decimalLatitude</value>
266
                                                        </_nullIf>
267
                                                    </latitude_deg>
268
                                                    <longitude_deg>
269
                                                        <_nullIf>
270
                                                            <null>0</null>
271
                                                            <type>float</type>
272
                                                            <value>$decimalLongitude</value>
273
                                                        </_nullIf>
274
                                                    </longitude_deg>
275
                                                </coordinates>
276
                                            </coordinates_id>
277
                                            <country>$country</country>
278
                                            <county>$county</county>
279
                                            <stateprovince>$stateProvince</stateprovince>
280
                                        </place>
281
                                    </matched_place_id>
282
                                    <stateprovince>$stateProvince</stateprovince>
283
                                </place>
284
                            </place_id>
285
                        </locationplace>
286
                        <notespublic>$locationRemarks</notespublic>
287
                        <verbatimelevation>$verbatimElevation</verbatimelevation>
288
                    </location>
289
                </path>
290
            </_simplifyPath>
291
        </path>
292
    </_setDefault>
293
</VegBIEN>
294
Inserted 39 new rows into database
inputs/HVAA/Specimen/new_terms.csv
1
symbiotaId,occurrenceID,,
inputs/HVAA/Specimen/unmapped_terms.csv
1
basisOfRecord
2
otherCatalogNumbers
3
ownerInstitutionCode
4
identificationReferences
5
identificationRemarks
6
typeStatus
7
year
8
month
9
day
10
startDayOfYear
11
endDayOfYear
12
verbatimEventDate
13
occurrenceRemarks
14
dynamicProperties
15
associatedTaxa
16
reproductiveCondition
17
lifeStage
18
preparations
19
municipality
20
geodeticDatum
21
*coordinatePrecision
22
verbatimCoordinateSystem
23
georeferencedBy
24
georeferenceProtocol
25
georeferenceSources
26
georeferenceVerificationStatus
27
georeferenceRemarks
28
disposition
29
modified
30
language
31
rightsHolder
inputs/HVAA/import_order.txt
1
Source
2
Specimen

Also available in: Unified diff